Reported missing the morning he was to meet with authorities investigating allegations that he molested a boy, the Rev. Alejandro Flores was found sprawled amid toppled pews at St. Mary's Carmelite Church in Joliet.

In an apparent attempt to take his life, Flores had plunged 20 feet from the choir loft, where investigators found an empty bottle of Johnny Walker Black Label scotch. They also discovered in his bedroom a suicide note he had written to one of the two brothers he was accused of molesting, according to police records.

"Dear son … Forgive me. I love you more than you know," Flores wrote in Spanish to the older boy.

A few days earlier, the mother of the boys had called the Diocese of Joliet to complain about the newly ordained priest's relationship with her younger son. The next morning, diocese officials promptly removed Flores from any contact with children and notified authorities, who later charged him with molesting the boy. Bishop J. Peter Sartain also publicly apologized to the child's family.

Although it appears the diocese may have responded swiftly in early 2010, the handling of the matter continues to draw criticism. And the scrutiny has followed Sartain to Seattle, where he was installed last winter as archbishop. Critics argue warning signs were ignored or missed while Flores was a seminary student — a five-year period that mostly occurred under Sartain's watch.

The case, investigators say, raises concerns about whether the diocese — which long faced allegations of covering up child sexual abuse by priests — withheld crucial information that should have been forwarded to police.

A Tribune examination found that at least three supervisors said they saw Flores alone with either one or both of the woman's sons several times before his June 2009 ordination, including once while the younger boy changed clothes in Flores' presence and was overheard calling him "Daddy," according to police reports, court records and interviews.Parishioners say they complained and that Flores ignored warnings that such contact wasn't appropriate.

The newspaper also learned Flores was sent for psychological evaluation and treatment at least twice, including three months before his ordination when he admitted viewing pornography on a parish computer, records show. Authorities said diocese officials later told them the images appeared to show young males engaged in sex acts.

Police said the diocese didn't report the questionable images, and that the computer's hard drive had disappeared when they sought it months later.

One priest who had supervised Flores was so frustrated that the seminarian was ordained despite repeated warnings that he wrote to Sartain asking why his complaints fell on deaf ears.

"Why have I not heard anything from you as my bishop?" the Rev. William Conway asked in the confidential letter obtained by the Tribune.

"Why was my input ignored...?" he wrote.

Flores, 38, is serving a four-year prison term for criminal sexual assault. He declined interview requests. Supporters say he maintains his innocence despite a guilty plea.

Flores was assigned to St. Mary Parish of West Chicago, where some parishioners said they are still outraged. One of them, Jennifer Wiesner, is a former St. Mary school board member.

"I'm disgusted to know that (church leaders) … knew Flores had an attraction for young boys, had a taste for them, and yet they irresponsibly still chose to knowingly put him at our school," she said.

Early warning signs

The Joliet diocese recruited Flores for the seminary in 2004 when he was living in Bolivia, where he was raised in an orphanage. He later studied theology and did missionary work, according to his profile in a diocese magazine.

By 2005, when Flores was assigned to St. Mary, he met an impoverished single mother from Mexico and her two young sons, then about 8 and 12. The first documented warning sign occurred that year when the Rev. Burke Masters, then an associate pastor, saw Flores alone in a car with the younger child and warned the seminary student it was not appropriate, records indicate.

Flores' contact with the boys grew so close during the next two years that several parishioners said they voiced their concerns to Conway, who was St. Mary's pastor, as well as to Masters and Flores himself. Parishioners Eduardo Fuentes and his wife, Luzma, of West Chicago, said Flores had the boys call him "Papa" and gave the oldest one expensive electronics, clothes and even a bike.

"They were together everywhere, all the time, to the extent that people were openly talking about it," Luzma Fuentes said.

In spring 2007, while she worked as a teacher's aide at a West Chicago welcome center for immigrant students, Fuentes and other workers there said they found suspicious emails between Flores and the oldest boy on a computer. They said he was a high school freshman at the time and often visited the center.

Masters, now the diocese's vocation director, and Conway, now pastor at a Downers Grove church, declined comment. But in a Sept. 14, 2010, letter to Sartain, Conway complained that his repeated concerns were ignored and that his opinion on Flores was never sought before the seminarian was ordained.

"During that time, there were different incidents that I brought to Fr. Masters' attention about Alex and the concerns that I had," Conway wrote. "I also recall telling Fr. Masters that I was worried that someday his trust in Alex might be betrayed."

Prosecutors said Flores' ordination was twice delayed, beginning in 2008 when he alleged he was abused years earlier in the Bolivian orphanage. It again was postponed in spring 2009 after the Rev. William Dewan, who supervised Flores during two internships at Holy Family Parish in Shorewood, said Flores admitted viewing pornography on a parish computer, according to a police report. Another psychological evaluation was ordered, a court record said.

Prosecutors said in a court document that Dewan also had seen Flores alone with the two brothers and that the younger child once changed his clothing in front of Flores.

"Father Dewan told the defendant that this was not appropriate behavior and he was not to be alone with minor children," Debra Bree, a Kane County prosecutor, said during Flores' plea hearing in September 2010. "He reported this information to Father Masters, who was in charge of seminary candidates including the defendant."

It's unclear whether Masters told Sartain of these concerns. Sartain allowed Flores' ordination three months after the pornography evaluation was ordered. Prosecutors said their efforts to learn the evaluation results were blocked.

Missing evidence

On Jan. 3, 2010, seven months after ordination, the mother of the two boys called Masters to report that her boyfriend said he saw Flores engage in suspicious activities with her younger son in a car and inside their St. Charles apartment after she allowed the priest to sleep there one night, according to court records.

Masters phoned Sartain the next morning. After speaking to Flores, Sartain transferred him to a diocese residence away from children and permanently removed him from his priestly duties. The diocese also alerted authorities.

The response differed from what happened during the tenure of Sartain's predecessor, retired Joliet Bishop Joseph Imesch, whose 27-year tenure was tarnished by a clergy sex abuse scandal.

Imesch faced accusations of failing to report repeated allegations of priest abuse to authorities. Critics accused him of transferring accused priests to new parishes after treatment and blocking police investigations.

Two days after the Flores allegations arose, and hours before he was to meet with Kane County investigators, diocese officials reported him missing to police. Soon afterward, authorities found Flores lying on the floor of St. Mary's Carmelite Church.

During their investigation, police uncovered another warning sign they said the diocese missed.

A former seminary student said he had a sexual affair with Flores that began in July 2007 inside the Shorewood church rectory while Dewan was out of town, according to police reports. The alleged affair lasted through 2009. The youth was 18 when it began. Flores was 34.

The two met at St. Mary's in West Chicago where the younger man was a parishioner. He told police Flores once gave him $3,000 as a gift, the report said.

Shorewood police Cmdr. Eric Allen said the younger man admitted deleting incriminating photos and stealing the camera's memory card from Flores' room to protect him while he was in the hospital recovering from the fall. Flores sustained critical head injuries but recovered.

Police said the young man "had direct knowledge of the charges against Flores and intentionally deleted photographs of Flores with young children laying together in bed," records show.

Allen said he was able to recover the memory card after the student cooperated and led him to a bush in Joliet where he had tossed it several weeks earlier.

Also disturbing, Allen said, was the diocese's handling of the spring 2009 pornography incident. Diocese officials never reported the questionable images despite concerns that minors were depicted because they said the website had a disclaimer saying only adults were featured, according to Allen. The images couldn't be retrieved months later when Allen became involved, he said.

"They said at some point someone got ahold of the hard drive and it disappeared," Allen said. "I told them, 'You had an obligation to contact the Police Department, and we'll make the determination if this is appropriate material or not.' It was disappointing how they handled it."

New flock, old issue

At his Sept. 8, 2010, guilty plea, Flores admitted abusing the youngest boy from 2005 to 2010, beginning when the child was 8, usually in his car or the family's St. Charles apartment. He faces deportation to Bolivia upon his release.

Days after Flores' plea, Sartain was named Seattle's new archbishop. A handful of protesters gathered outside the cathedral at his Dec. 1 installation.

The Survivors Network of those Abused by Priests (SNAP) called for Pope Benedict XVI to revoke the appointment based on the Flores case. Though it's not clear how much Sartain knew, critics argue it was enough not to ordain Flores.

Under the direction of Bishop R. Daniel Conlon, the current head of the Joliet Diocese, the diocese is negotiating with the family of the two boys to try to reach a settlement, according to the family's attorney.

In hindsight, Flores shouldn't have been ordained, Doug Delaney, a spokesman for the diocese, said shortly after the guilty plea.

In a recent statement to the Tribune, Sartain again apologized for the abuse.

"Once again, I express my deepest apologies to these young boys and their family for the suffering they are experiencing as a result of this abuse," Sartain said. "Their trust has been broken, and this is a terrible tragedy for them and for the church."